Macromolecule Content

Total Structure Weight: 111.09 kDa
Atom Count: 7,764
Modelled Residue Count: 980
Deposited Residue Count: 988
Unique protein chains: 1

2OTD

The crystal structure of the glycerophosphodiester phosphodiesterase from Shigella flexneri 2a

PDB DOI: https://doi.org/10.2210/pdb2OTD/pdb

Classification: HYDROLASE
Organism(s): Shigella flexneri
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2007-02-07 Released: 2007-03-06
Deposition Author(s): Zhang, R., Wu, R., Clancy, S., Jiang, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.276
R-Value Work: 0.221
R-Value Observed: 0.224

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of the glycerophosphodiester phosphodiesterase from Shigella flexneri 2a

Zhang, R., Wu, R., Clancy, S., Jiang, S., Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerophosphodiester phosphodiesterase	A, B, C, D	247	Shigella flexneri	Mutation(s): 7 Gene Names: ugpQ, SF3466, S_4296 EC: 3.1.4.1
UniProt
Find proteins for A0A0H2V2B5 (Shigella flexneri) Explore A0A0H2V2B5 Go to UniProtKB: A0A0H2V2B5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2V2B5
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.276
R-Value Work: 0.221
R-Value Observed: 0.224
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.617	α = 90
b = 82.185	β = 90
c = 223.202	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-03-06

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-03-06
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.